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<li class="toctree-l1"><a class="reference internal" href="index.html">Introduction</a></li>
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<li class="toctree-l2"><a class="reference internal" href="tutorials/gcnn_tutorial.html">GraphCNN for predicting logP</a><ul>
<li class="toctree-l3"><a class="reference internal" href="tutorials/gcnn_tutorial.html#defining-node-attributes">Defining node attributes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="api-docs/blocks.html">API documentation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="api-docs/models.html">models</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api-docs/models.html#module-models.openchem_model">openchem_model</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/models.html#module-models.Smiles2Label">Smiles2Label</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/models.html#module-models.Graph2Label">Graph2Label</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/models.html#module-models.MoleculeProtein2Label">MoleculeProtein2Label</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/models.html#vanilla-model">vanilla_model</a></li>
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<li class="toctree-l4"><a class="reference internal" href="api-docs/modules.encoders.html#module-modules.encoders.openchem_encoder">openchem_encoder</a></li>
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<li class="toctree-l3"><a class="reference internal" href="api-docs/modules.embeddings.html">embeddings</a><ul>
<li class="toctree-l4"><a class="reference internal" href="api-docs/modules.embeddings.html#module-modules.embeddings.openchem_embedding">openchem_embedding</a></li>
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<li class="toctree-l3"><a class="reference internal" href="api-docs/modules.mlp.html">mlp</a></li>
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<li class="toctree-l3"><a class="reference internal" href="api-docs/layers.html#module-layers.conv_bn_relu">conv_bn_relu</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/layers.html#module-layers.gcn">gcn</a></li>
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<li class="toctree-l2"><a class="reference internal" href="api-docs/data.html">data</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api-docs/data.html#module-data.smiles_data_layer">smiles_data_layer</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/data.html#graph-data-layer">graph_data_layer</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/data.html#module-data.smiles_protein_data_layer">smiles_protein_data_layer</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/data.html#module-data.vanilla_data_layer">vanilla_data_layer</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/data.html#module-data.smiles_enumerator">smiles_enumerator</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/data.html#module-data.utils">utils</a></li>
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<li class="toctree-l2"><a class="reference internal" href="api-docs/criterion.html">criterion</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api-docs/criterion.html#module-openchem.criterion.multitask_loss">multitask_loss</a></li>
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<li class="toctree-l2"><a class="reference internal" href="api-docs/optimizer.html">optimizer</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api-docs/optimizer.html#module-optimizer.openchem_optimizer">openchem_optimizer</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/optimizer.html#module-optimizer.openchem_lr_scheduler">openchem_lr_scheduler</a></li>
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<li class="toctree-l2"><a class="reference internal" href="api-docs/utils.html">utils</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api-docs/utils.html#module-openchem.utils.graph">graph</a></li>
<li class="toctree-l3"><a class="reference internal" href="api-docs/utils.html#id1">utils</a></li>
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<h1 id="index">Index</h1>

<div class="genindex-jumpbox">
 <a href="#A"><strong>A</strong></a>
 | <a href="#B"><strong>B</strong></a>
 | <a href="#C"><strong>C</strong></a>
 | <a href="#D"><strong>D</strong></a>
 | <a href="#E"><strong>E</strong></a>
 | <a href="#F"><strong>F</strong></a>
 | <a href="#G"><strong>G</strong></a>
 | <a href="#I"><strong>I</strong></a>
 | <a href="#L"><strong>L</strong></a>
 | <a href="#M"><strong>M</strong></a>
 | <a href="#N"><strong>N</strong></a>
 | <a href="#O"><strong>O</strong></a>
 | <a href="#P"><strong>P</strong></a>
 | <a href="#R"><strong>R</strong></a>
 | <a href="#S"><strong>S</strong></a>
 | <a href="#T"><strong>T</strong></a>
 | <a href="#V"><strong>V</strong></a>
 | <a href="#X"><strong>X</strong></a>
 | <a href="#Z"><strong>Z</strong></a>
 
</div>
<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/utils.html#openchem.utils.graph.Attribute">Attribute (class in openchem.utils.graph)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/data.html#data.utils.augment_smiles">augment_smiles() (in module data.utils)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/models.html#models.openchem_model.build_training">build_training() (in module models.openchem_model)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_lr_scheduler.OpenChemLRScheduler.by_iteration">by_iteration() (optimizer.openchem_lr_scheduler.OpenChemLRScheduler property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/utils.html#openchem.utils.utils.calculate_metrics">calculate_metrics() (in module openchem.utils.utils)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.canonize_smiles">canonize_smiles() (in module data.utils)</a>
</li>
      <li><a href="api-docs/models.html#models.Graph2Label.Graph2Label.cast_inputs">cast_inputs() (models.Graph2Label.Graph2Label static method)</a>

      <ul>
        <li><a href="api-docs/models.html#models.MoleculeProtein2Label.MoleculeProtein2Label.cast_inputs">(models.MoleculeProtein2Label.MoleculeProtein2Label method)</a>
</li>
        <li><a href="api-docs/models.html#models.openchem_model.OpenChemModel.cast_inputs">(models.openchem_model.OpenChemModel static method)</a>
</li>
        <li><a href="api-docs/models.html#models.Smiles2Label.Smiles2Label.cast_inputs">(models.Smiles2Label.Smiles2Label static method)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/data.html#data.smiles_enumerator.SmilesEnumerator.charset">charset() (data.smiles_enumerator.SmilesEnumerator property)</a>
</li>
      <li><a href="api-docs/utils.html#openchem.utils.utils.check_params">check_params() (in module openchem.utils.utils)</a>
</li>
      <li><a href="api-docs/layers.html#layers.conv_bn_relu.ConvBNReLU">ConvBNReLU (class in layers.conv_bn_relu)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.create_loader">create_loader() (in module data.utils)</a>
</li>
      <li><a href="api-docs/utils.html#openchem.utils.utils.cross_validation_split">cross_validation_split() (in module openchem.utils.utils)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.cut_padding">cut_padding() (in module data.utils)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li>
    data

      <ul>
        <li><a href="api-docs/data.html#module-data">module</a>
</li>
      </ul></li>
      <li>
    data.smiles_data_layer

      <ul>
        <li><a href="api-docs/data.html#module-data.smiles_data_layer">module</a>
</li>
      </ul></li>
      <li>
    data.smiles_enumerator

      <ul>
        <li><a href="api-docs/data.html#module-data.smiles_enumerator">module</a>
</li>
      </ul></li>
      <li>
    data.smiles_protein_data_layer

      <ul>
        <li><a href="api-docs/data.html#module-data.smiles_protein_data_layer">module</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li>
    data.utils

      <ul>
        <li><a href="api-docs/data.html#module-data.utils">module</a>
</li>
      </ul></li>
      <li>
    data.vanilla_data_layer

      <ul>
        <li><a href="api-docs/data.html#module-data.vanilla_data_layer">module</a>
</li>
      </ul></li>
      <li><a href="api-docs/utils.html#openchem.utils.utils.deco_print">deco_print() (in module openchem.utils.utils)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.DummyDataLoader">DummyDataLoader (class in data.utils)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.DummyDataset">DummyDataset (class in data.utils)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/utils.html#openchem.utils.graph.Edge">Edge (class in openchem.utils.graph)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/modules.embeddings.html#modules.embeddings.basic_embedding.Embedding">Embedding (class in modules.embeddings.basic_embedding)</a>
</li>
      <li><a href="api-docs/models.html#models.openchem_model.evaluate">evaluate() (in module models.openchem_model)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/data.html#data.smiles_enumerator.SmilesEnumerator.fit">fit() (data.smiles_enumerator.SmilesEnumerator method)</a>

      <ul>
        <li><a href="api-docs/models.html#models.openchem_model.fit">(in module models.openchem_model)</a>
</li>
      </ul></li>
      <li><a href="api-docs/utils.html#openchem.utils.utils.flatten_dict">flatten_dict() (in module openchem.utils.utils)</a>
</li>
      <li><a href="api-docs/layers.html#layers.conv_bn_relu.ConvBNReLU.forward">forward() (layers.conv_bn_relu.ConvBNReLU method)</a>

      <ul>
        <li><a href="api-docs/layers.html#layers.gcn.GraphConvolution.forward">(layers.gcn.GraphConvolution method)</a>
</li>
        <li><a href="api-docs/models.html#models.Graph2Label.Graph2Label.forward">(models.Graph2Label.Graph2Label method)</a>
</li>
        <li><a href="api-docs/models.html#models.MoleculeProtein2Label.MoleculeProtein2Label.forward">(models.MoleculeProtein2Label.MoleculeProtein2Label method)</a>
</li>
        <li><a href="api-docs/models.html#models.openchem_model.OpenChemModel.forward">(models.openchem_model.OpenChemModel method)</a>
</li>
        <li><a href="api-docs/models.html#models.Smiles2Label.Smiles2Label.forward">(models.Smiles2Label.Smiles2Label method)</a>
</li>
        <li><a href="api-docs/modules.embeddings.html#modules.embeddings.basic_embedding.Embedding.forward">(modules.embeddings.basic_embedding.Embedding method)</a>
</li>
        <li><a href="api-docs/modules.embeddings.html#modules.embeddings.openchem_embedding.OpenChemEmbedding.forward">(modules.embeddings.openchem_embedding.OpenChemEmbedding method)</a>
</li>
        <li><a href="api-docs/modules.encoders.html#modules.encoders.openchem_encoder.OpenChemEncoder.forward">(modules.encoders.openchem_encoder.OpenChemEncoder method)</a>
</li>
        <li><a href="api-docs/modules.encoders.html#modules.encoders.rnn_encoder.RNNEncoder.forward">(modules.encoders.rnn_encoder.RNNEncoder method)</a>
</li>
        <li><a href="api-docs/modules.mlp.html#modules.mlp.openchem_mlp.OpenChemMLP.forward">(modules.mlp.openchem_mlp.OpenChemMLP method)</a>
</li>
        <li><a href="api-docs/modules.mlp.html#modules.mlp.openchem_mlp.OpenChemMLPSimple.forward">(modules.mlp.openchem_mlp.OpenChemMLPSimple method)</a>
</li>
        <li><a href="api-docs/criterion.html#openchem.criterion.multitask_loss.MultitaskLoss.forward">(openchem.criterion.multitask_loss.MultitaskLoss method)</a>
</li>
      </ul></li>
  </ul></td>
</tr></table>

<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/utils.html#openchem.utils.graph.Graph.get_edge_attr_adj_matrix">get_edge_attr_adj_matrix() (openchem.utils.graph.Graph method)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.get_fp">get_fp() (in module data.utils)</a>
</li>
      <li><a href="api-docs/utils.html#openchem.utils.utils.get_latest_checkpoint">get_latest_checkpoint() (in module openchem.utils.utils)</a>
</li>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_optimizer.OpenChemOptimizer.get_lr">get_lr() (optimizer.openchem_optimizer.OpenChemOptimizer method)</a>
</li>
      <li><a href="api-docs/utils.html#openchem.utils.graph.Graph.get_node_attr_adj_matrix">get_node_attr_adj_matrix() (openchem.utils.graph.Graph method)</a>
</li>
      <li><a href="api-docs/utils.html#openchem.utils.graph.Graph.get_node_feature_matrix">get_node_feature_matrix() (openchem.utils.graph.Graph method)</a>
</li>
      <li><a href="api-docs/models.html#models.openchem_model.OpenChemModel.get_optional_params">get_optional_params() (models.openchem_model.OpenChemModel static method)</a>

      <ul>
        <li><a href="api-docs/modules.embeddings.html#modules.embeddings.openchem_embedding.OpenChemEmbedding.get_optional_params">(modules.embeddings.openchem_embedding.OpenChemEmbedding static method)</a>
</li>
        <li><a href="api-docs/modules.encoders.html#modules.encoders.openchem_encoder.OpenChemEncoder.get_optional_params">(modules.encoders.openchem_encoder.OpenChemEncoder static method)</a>
</li>
        <li><a href="api-docs/modules.encoders.html#modules.encoders.rnn_encoder.RNNEncoder.get_optional_params">(modules.encoders.rnn_encoder.RNNEncoder static method)</a>
</li>
        <li><a href="api-docs/modules.mlp.html#modules.mlp.openchem_mlp.OpenChemMLP.get_optional_params">(modules.mlp.openchem_mlp.OpenChemMLP static method)</a>
</li>
        <li><a href="api-docs/modules.mlp.html#modules.mlp.openchem_mlp.OpenChemMLPSimple.get_optional_params">(modules.mlp.openchem_mlp.OpenChemMLPSimple static method)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/models.html#models.openchem_model.OpenChemModel.get_required_params">get_required_params() (models.openchem_model.OpenChemModel static method)</a>

      <ul>
        <li><a href="api-docs/modules.embeddings.html#modules.embeddings.basic_embedding.Embedding.get_required_params">(modules.embeddings.basic_embedding.Embedding static method)</a>
</li>
        <li><a href="api-docs/modules.embeddings.html#modules.embeddings.openchem_embedding.OpenChemEmbedding.get_required_params">(modules.embeddings.openchem_embedding.OpenChemEmbedding static method)</a>
</li>
        <li><a href="api-docs/modules.encoders.html#modules.encoders.openchem_encoder.OpenChemEncoder.get_required_params">(modules.encoders.openchem_encoder.OpenChemEncoder static method)</a>
</li>
        <li><a href="api-docs/modules.encoders.html#modules.encoders.rnn_encoder.RNNEncoder.get_required_params">(modules.encoders.rnn_encoder.RNNEncoder static method)</a>
</li>
        <li><a href="api-docs/modules.mlp.html#modules.mlp.openchem_mlp.OpenChemMLP.get_required_params">(modules.mlp.openchem_mlp.OpenChemMLP static method)</a>
</li>
        <li><a href="api-docs/modules.mlp.html#modules.mlp.openchem_mlp.OpenChemMLPSimple.get_required_params">(modules.mlp.openchem_mlp.OpenChemMLPSimple static method)</a>
</li>
      </ul></li>
      <li><a href="api-docs/data.html#data.utils.get_tokens">get_tokens() (in module data.utils)</a>
</li>
      <li><a href="api-docs/utils.html#openchem.utils.graph.Graph">Graph (class in openchem.utils.graph)</a>
</li>
      <li><a href="api-docs/models.html#models.Graph2Label.Graph2Label">Graph2Label (class in models.Graph2Label)</a>
</li>
      <li><a href="api-docs/layers.html#layers.gcn.GraphConvolution">GraphConvolution (class in layers.gcn)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="I">I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/utils.html#openchem.utils.utils.identity">identity() (in module openchem.utils.utils)</a>
</li>
      <li><a href="api-docs/modules.encoders.html#modules.encoders.rnn_encoder.RNNEncoder.init_cell">init_cell() (modules.encoders.rnn_encoder.RNNEncoder method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/modules.encoders.html#modules.encoders.rnn_encoder.RNNEncoder.init_hidden">init_hidden() (modules.encoders.rnn_encoder.RNNEncoder method)</a>
</li>
      <li><a href="api-docs/data.html#data.smiles_enumerator.Iterator">Iterator (class in data.smiles_enumerator)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li>
    layers

      <ul>
        <li><a href="api-docs/layers.html#module-layers">module</a>
</li>
      </ul></li>
      <li>
    layers.conv_bn_relu

      <ul>
        <li><a href="api-docs/layers.html#module-layers.conv_bn_relu">module</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li>
    layers.gcn

      <ul>
        <li><a href="api-docs/layers.html#module-layers.gcn">module</a>
</li>
      </ul></li>
      <li><a href="api-docs/models.html#models.openchem_model.OpenChemModel.load_model">load_model() (models.openchem_model.OpenChemModel method)</a>
</li>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_optimizer.OpenChemOptimizer.load_state_dict">load_state_dict() (optimizer.openchem_optimizer.OpenChemOptimizer method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/utils.html#openchem.utils.utils.make_positions">make_positions() (in module openchem.utils.utils)</a>
</li>
      <li>
    models

      <ul>
        <li><a href="api-docs/models.html#module-models">module</a>
</li>
      </ul></li>
      <li>
    models.Graph2Label

      <ul>
        <li><a href="api-docs/models.html#module-models.Graph2Label">module</a>
</li>
      </ul></li>
      <li>
    models.MoleculeProtein2Label

      <ul>
        <li><a href="api-docs/models.html#module-models.MoleculeProtein2Label">module</a>
</li>
      </ul></li>
      <li>
    models.openchem_model

      <ul>
        <li><a href="api-docs/models.html#module-models.openchem_model">module</a>
</li>
      </ul></li>
      <li>
    models.Smiles2Label

      <ul>
        <li><a href="api-docs/models.html#module-models.Smiles2Label">module</a>
</li>
      </ul></li>
      <li>
    module

      <ul>
        <li><a href="api-docs/data.html#module-data">data</a>
</li>
        <li><a href="api-docs/data.html#module-data.smiles_data_layer">data.smiles_data_layer</a>
</li>
        <li><a href="api-docs/data.html#module-data.smiles_enumerator">data.smiles_enumerator</a>
</li>
        <li><a href="api-docs/data.html#module-data.smiles_protein_data_layer">data.smiles_protein_data_layer</a>
</li>
        <li><a href="api-docs/data.html#module-data.utils">data.utils</a>
</li>
        <li><a href="api-docs/data.html#module-data.vanilla_data_layer">data.vanilla_data_layer</a>
</li>
        <li><a href="api-docs/layers.html#module-layers">layers</a>
</li>
        <li><a href="api-docs/layers.html#module-layers.conv_bn_relu">layers.conv_bn_relu</a>
</li>
        <li><a href="api-docs/layers.html#module-layers.gcn">layers.gcn</a>
</li>
        <li><a href="api-docs/models.html#module-models">models</a>
</li>
        <li><a href="api-docs/models.html#module-models.Graph2Label">models.Graph2Label</a>
</li>
        <li><a href="api-docs/models.html#module-models.MoleculeProtein2Label">models.MoleculeProtein2Label</a>
</li>
        <li><a href="api-docs/models.html#module-models.openchem_model">models.openchem_model</a>
</li>
        <li><a href="api-docs/models.html#module-models.Smiles2Label">models.Smiles2Label</a>
</li>
        <li><a href="api-docs/modules.html#module-modules">modules</a>
</li>
        <li><a href="api-docs/modules.embeddings.html#module-modules.embeddings">modules.embeddings</a>
</li>
        <li><a href="api-docs/modules.embeddings.html#module-modules.embeddings.basic_embedding">modules.embeddings.basic_embedding</a>
</li>
        <li><a href="api-docs/modules.embeddings.html#module-modules.embeddings.openchem_embedding">modules.embeddings.openchem_embedding</a>
</li>
        <li><a href="api-docs/modules.encoders.html#module-modules.encoders">modules.encoders</a>
</li>
        <li><a href="api-docs/modules.encoders.html#module-modules.encoders.openchem_encoder">modules.encoders.openchem_encoder</a>
</li>
        <li><a href="api-docs/modules.encoders.html#module-modules.encoders.rnn_encoder">modules.encoders.rnn_encoder</a>
</li>
        <li><a href="api-docs/modules.mlp.html#module-modules.mlp.openchem_mlp">modules.mlp.openchem_mlp</a>
</li>
        <li><a href="api-docs/criterion.html#module-openchem.criterion">openchem.criterion</a>
</li>
        <li><a href="api-docs/criterion.html#module-openchem.criterion.multitask_loss">openchem.criterion.multitask_loss</a>
</li>
        <li><a href="api-docs/utils.html#module-openchem.utils">openchem.utils</a>
</li>
        <li><a href="api-docs/utils.html#module-openchem.utils.graph">openchem.utils.graph</a>
</li>
        <li><a href="api-docs/utils.html#module-openchem.utils.utils">openchem.utils.utils</a>
</li>
        <li><a href="api-docs/optimizer.html#module-optimizer">optimizer</a>
</li>
        <li><a href="api-docs/optimizer.html#module-optimizer.openchem_lr_scheduler">optimizer.openchem_lr_scheduler</a>
</li>
        <li><a href="api-docs/optimizer.html#module-optimizer.openchem_optimizer">optimizer.openchem_optimizer</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li>
    modules

      <ul>
        <li><a href="api-docs/modules.html#module-modules">module</a>
</li>
      </ul></li>
      <li>
    modules.embeddings

      <ul>
        <li><a href="api-docs/modules.embeddings.html#module-modules.embeddings">module</a>
</li>
      </ul></li>
      <li>
    modules.embeddings.basic_embedding

      <ul>
        <li><a href="api-docs/modules.embeddings.html#module-modules.embeddings.basic_embedding">module</a>
</li>
      </ul></li>
      <li>
    modules.embeddings.openchem_embedding

      <ul>
        <li><a href="api-docs/modules.embeddings.html#module-modules.embeddings.openchem_embedding">module</a>
</li>
      </ul></li>
      <li>
    modules.encoders

      <ul>
        <li><a href="api-docs/modules.encoders.html#module-modules.encoders">module</a>
</li>
      </ul></li>
      <li>
    modules.encoders.openchem_encoder

      <ul>
        <li><a href="api-docs/modules.encoders.html#module-modules.encoders.openchem_encoder">module</a>
</li>
      </ul></li>
      <li>
    modules.encoders.rnn_encoder

      <ul>
        <li><a href="api-docs/modules.encoders.html#module-modules.encoders.rnn_encoder">module</a>
</li>
      </ul></li>
      <li>
    modules.mlp.openchem_mlp

      <ul>
        <li><a href="api-docs/modules.mlp.html#module-modules.mlp.openchem_mlp">module</a>
</li>
      </ul></li>
      <li><a href="api-docs/data.html#data.utils.mol2image">mol2image() (in module data.utils)</a>
</li>
      <li><a href="api-docs/models.html#models.MoleculeProtein2Label.MoleculeProtein2Label">MoleculeProtein2Label (class in models.MoleculeProtein2Label)</a>
</li>
      <li><a href="api-docs/utils.html#openchem.utils.utils.move_to_cuda">move_to_cuda() (in module openchem.utils.utils)</a>
</li>
      <li><a href="api-docs/criterion.html#openchem.criterion.multitask_loss.MultitaskLoss">MultitaskLoss (class in openchem.criterion.multitask_loss)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/utils.html#openchem.utils.utils.nest_dict">nest_dict() (in module openchem.utils.utils)</a>
</li>
      <li><a href="api-docs/utils.html#openchem.utils.utils.nested_update">nested_update() (in module openchem.utils.utils)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/data.html#data.smiles_enumerator.SmilesIterator.next">next() (data.smiles_enumerator.SmilesIterator method)</a>
</li>
      <li><a href="api-docs/utils.html#openchem.utils.graph.Node">Node (class in openchem.utils.graph)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="O">O</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li>
    openchem.criterion

      <ul>
        <li><a href="api-docs/criterion.html#module-openchem.criterion">module</a>
</li>
      </ul></li>
      <li>
    openchem.criterion.multitask_loss

      <ul>
        <li><a href="api-docs/criterion.html#module-openchem.criterion.multitask_loss">module</a>
</li>
      </ul></li>
      <li>
    openchem.utils

      <ul>
        <li><a href="api-docs/utils.html#module-openchem.utils">module</a>
</li>
      </ul></li>
      <li>
    openchem.utils.graph

      <ul>
        <li><a href="api-docs/utils.html#module-openchem.utils.graph">module</a>
</li>
      </ul></li>
      <li>
    openchem.utils.utils

      <ul>
        <li><a href="api-docs/utils.html#module-openchem.utils.utils">module</a>
</li>
      </ul></li>
      <li><a href="api-docs/modules.embeddings.html#modules.embeddings.openchem_embedding.OpenChemEmbedding">OpenChemEmbedding (class in modules.embeddings.openchem_embedding)</a>
</li>
      <li><a href="api-docs/modules.encoders.html#modules.encoders.openchem_encoder.OpenChemEncoder">OpenChemEncoder (class in modules.encoders.openchem_encoder)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_lr_scheduler.OpenChemLRScheduler">OpenChemLRScheduler (class in optimizer.openchem_lr_scheduler)</a>
</li>
      <li><a href="api-docs/modules.mlp.html#modules.mlp.openchem_mlp.OpenChemMLP">OpenChemMLP (class in modules.mlp.openchem_mlp)</a>
</li>
      <li><a href="api-docs/modules.mlp.html#modules.mlp.openchem_mlp.OpenChemMLPSimple">OpenChemMLPSimple (class in modules.mlp.openchem_mlp)</a>
</li>
      <li><a href="api-docs/models.html#models.openchem_model.OpenChemModel">OpenChemModel (class in models.openchem_model)</a>
</li>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_optimizer.OpenChemOptimizer">OpenChemOptimizer (class in optimizer.openchem_optimizer)</a>
</li>
      <li>
    optimizer

      <ul>
        <li><a href="api-docs/optimizer.html#module-optimizer">module</a>
</li>
      </ul></li>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_optimizer.OpenChemOptimizer.optimizer">optimizer() (optimizer.openchem_optimizer.OpenChemOptimizer property)</a>
</li>
      <li>
    optimizer.openchem_lr_scheduler

      <ul>
        <li><a href="api-docs/optimizer.html#module-optimizer.openchem_lr_scheduler">module</a>
</li>
      </ul></li>
      <li>
    optimizer.openchem_optimizer

      <ul>
        <li><a href="api-docs/optimizer.html#module-optimizer.openchem_optimizer">module</a>
</li>
      </ul></li>
  </ul></td>
</tr></table>

<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/data.html#data.utils.pad_sequences">pad_sequences() (in module data.utils)</a>
</li>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_optimizer.OpenChemOptimizer.param_groups">param_groups() (optimizer.openchem_optimizer.OpenChemOptimizer property)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/models.html#models.openchem_model.predict">predict() (in module models.openchem_model)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.process_graphs">process_graphs() (in module data.utils)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.process_smiles">process_smiles() (in module data.utils)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/data.html#data.smiles_enumerator.SmilesEnumerator.randomize_smiles">randomize_smiles() (data.smiles_enumerator.SmilesEnumerator method)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.read_smi_file">read_smi_file() (in module data.utils)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.read_smiles_property_file">read_smiles_property_file() (in module data.utils)</a>
</li>
      <li><a href="api-docs/models.html#models.openchem_model.reduce_tensor">reduce_tensor() (in module models.openchem_model)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/criterion.html#openchem.criterion.multitask_loss.MultitaskLoss.reduction">reduction (openchem.criterion.multitask_loss.MultitaskLoss attribute)</a>
</li>
      <li><a href="api-docs/data.html#data.smiles_enumerator.Iterator.reset">reset() (data.smiles_enumerator.Iterator method)</a>
</li>
      <li><a href="api-docs/layers.html#layers.gcn.GraphConvolution.reset_parameters">reset_parameters() (layers.gcn.GraphConvolution method)</a>
</li>
      <li><a href="api-docs/data.html#data.smiles_enumerator.SmilesEnumerator.reverse_transform">reverse_transform() (data.smiles_enumerator.SmilesEnumerator method)</a>
</li>
      <li><a href="api-docs/modules.encoders.html#modules.encoders.rnn_encoder.RNNEncoder">RNNEncoder (class in modules.encoders.rnn_encoder)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/data.html#data.utils.sanitize_smiles">sanitize_smiles() (in module data.utils)</a>
</li>
      <li><a href="api-docs/models.html#models.openchem_model.OpenChemModel.save_model">save_model() (models.openchem_model.OpenChemModel method)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.save_smi_to_file">save_smi_to_file() (in module data.utils)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.save_smiles_property_file">save_smiles_property_file() (in module data.utils)</a>
</li>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_lr_scheduler.OpenChemLRScheduler.scheduler">scheduler() (optimizer.openchem_lr_scheduler.OpenChemLRScheduler property)</a>
</li>
      <li><a href="api-docs/data.html#data.utils.seq2tensor">seq2tensor() (in module data.utils)</a>
</li>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_optimizer.OpenChemOptimizer.set_lr">set_lr() (optimizer.openchem_optimizer.OpenChemOptimizer method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/models.html#models.Smiles2Label.Smiles2Label">Smiles2Label (class in models.Smiles2Label)</a>
</li>
      <li><a href="api-docs/data.html#data.smiles_data_layer.SmilesDataset">SmilesDataset (class in data.smiles_data_layer)</a>
</li>
      <li><a href="api-docs/data.html#data.smiles_enumerator.SmilesEnumerator">SmilesEnumerator (class in data.smiles_enumerator)</a>
</li>
      <li><a href="api-docs/data.html#data.smiles_enumerator.SmilesIterator">SmilesIterator (class in data.smiles_enumerator)</a>
</li>
      <li><a href="api-docs/data.html#data.smiles_protein_data_layer.SmilesProteinDataset">SmilesProteinDataset (class in data.smiles_protein_data_layer)</a>
</li>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_optimizer.OpenChemOptimizer.state_dict">state_dict() (optimizer.openchem_optimizer.OpenChemOptimizer method)</a>
</li>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_lr_scheduler.OpenChemLRScheduler.step">step() (optimizer.openchem_lr_scheduler.OpenChemLRScheduler method)</a>

      <ul>
        <li><a href="api-docs/optimizer.html#optimizer.openchem_optimizer.OpenChemOptimizer.step">(optimizer.openchem_optimizer.OpenChemOptimizer method)</a>
</li>
      </ul></li>
  </ul></td>
</tr></table>

<h2 id="T">T</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/data.html#data.utils.time_since">time_since() (in module data.utils)</a>

      <ul>
        <li><a href="api-docs/utils.html#openchem.utils.utils.time_since">(in module openchem.utils.utils)</a>
</li>
      </ul></li>
      <li><a href="api-docs/models.html#models.openchem_model.train_step">train_step() (in module models.openchem_model)</a>
</li>
      <li><a href="api-docs/layers.html#layers.conv_bn_relu.ConvBNReLU.training">training (layers.conv_bn_relu.ConvBNReLU attribute)</a>

      <ul>
        <li><a href="api-docs/layers.html#layers.gcn.GraphConvolution.training">(layers.gcn.GraphConvolution attribute)</a>
</li>
        <li><a href="api-docs/models.html#models.Graph2Label.Graph2Label.training">(models.Graph2Label.Graph2Label attribute)</a>
</li>
        <li><a href="api-docs/models.html#models.MoleculeProtein2Label.MoleculeProtein2Label.training">(models.MoleculeProtein2Label.MoleculeProtein2Label attribute)</a>
</li>
        <li><a href="api-docs/models.html#models.openchem_model.OpenChemModel.training">(models.openchem_model.OpenChemModel attribute)</a>
</li>
        <li><a href="api-docs/models.html#models.Smiles2Label.Smiles2Label.training">(models.Smiles2Label.Smiles2Label attribute)</a>
</li>
        <li><a href="api-docs/modules.embeddings.html#modules.embeddings.basic_embedding.Embedding.training">(modules.embeddings.basic_embedding.Embedding attribute)</a>
</li>
        <li><a href="api-docs/modules.embeddings.html#modules.embeddings.openchem_embedding.OpenChemEmbedding.training">(modules.embeddings.openchem_embedding.OpenChemEmbedding attribute)</a>
</li>
        <li><a href="api-docs/modules.encoders.html#modules.encoders.openchem_encoder.OpenChemEncoder.training">(modules.encoders.openchem_encoder.OpenChemEncoder attribute)</a>
</li>
        <li><a href="api-docs/modules.encoders.html#modules.encoders.rnn_encoder.RNNEncoder.training">(modules.encoders.rnn_encoder.RNNEncoder attribute)</a>
</li>
        <li><a href="api-docs/modules.mlp.html#modules.mlp.openchem_mlp.OpenChemMLP.training">(modules.mlp.openchem_mlp.OpenChemMLP attribute)</a>
</li>
        <li><a href="api-docs/modules.mlp.html#modules.mlp.openchem_mlp.OpenChemMLPSimple.training">(modules.mlp.openchem_mlp.OpenChemMLPSimple attribute)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/data.html#data.smiles_enumerator.SmilesEnumerator.transform">transform() (data.smiles_enumerator.SmilesEnumerator method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="V">V</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/data.html#data.vanilla_data_layer.VanillaDataset">VanillaDataset (class in data.vanilla_data_layer)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="X">X</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/utils.html#openchem.utils.graph.Graph.xyz_to_zmat">xyz_to_zmat() (openchem.utils.graph.Graph method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="Z">Z</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/optimizer.html#optimizer.openchem_optimizer.OpenChemOptimizer.zero_grad">zero_grad() (optimizer.openchem_optimizer.OpenChemOptimizer method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="api-docs/utils.html#openchem.utils.graph.Graph.zmat_to_xyz">zmat_to_xyz() (openchem.utils.graph.Graph method)</a>
</li>
  </ul></td>
</tr></table>



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